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bug fixed in collapse, now work with collapse a clade that contain a subclade that was already collapsed

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118094 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 02/06/2016 03:29:16
Showing 2 changed files

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@@ -1,5 +1,6 @@
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 CHANGES IN VERSION 1.5.5
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+ o bug fixed in collapse, now work with collapse a clade that contain a subclade that was already collapsed <2016-06-02-Thu>
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  o bug fixed if time-scaled tree extend into the BCE. <2016-06-02, Thu>
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    + as.Date won't work for BCE time.
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    + as.Date=FALSE by default in fortify method, just use the time in decimal format (real number, not Date object).
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@@ -60,7 +60,7 @@ collapse <- function(tree_view=NULL, node) {
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     sp <- get.offspring.df(df, node)
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     sp.df <- df[sp,]
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     df[node, "isTip"] <- TRUE
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-    sp_y <- range(sp.df$y)
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+    sp_y <- range(sp.df$y, na.rm=TRUE)
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     ii <- which(df$y > max(sp_y))
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     if (length(ii)) {
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         df$y[ii] <- df$y[ii] - diff(sp_y)